CoV-GLUE | Mutations | Mutation
Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):
ORF | CodonNum | Mut | ORF1abMut | MutType | RefCodon | MutCodon | AACount | CodonCount | CodonProp | Genome Position |
S | 80 | D80A | nonsyn | gAt | gCt | 40300 | 40298 | 0.99995 | 21800-21802 |
Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):
ORF | CodonNum | Mut | RefCodon | MutCodon | CodonCount | AACount | Lineage | LineageCodonProp |
S | 80 | D80A | gAt | gCt | 40298 | 40300 | All | 0.007707 |
S | 80 | D80A | gAt | gCt | 33030 | 33031 | B.1.351 | 0.981867 |
S | 80 | D80A | gAt | gCt | 3299 | 3299 | B.1.351.2 | 0.998185 |
S | 80 | D80A | gAt | gCt | 1665 | 1665 | B.1.351.5 | 0.998201 |
S | 80 | D80A | gAt | gCt | 1139 | 1139 | B.1.351.3 | 0.998247 |
S | 80 | D80A | gAt | gCt | 484 | 484 | B.1 | 0.004433 |
S | 80 | D80A | gAt | gCt | 52 | 52 | B.1.524 | 0.073136 |
S | 80 | D80A | gAt | gCt | 47 | 47 | AY.45 | 0.005719 |
S | 80 | D80A | gAt | gCt | 44 | 44 | B.1.617.2 | 0.000166 |
S | 80 | D80A | gAt | gCt | 32 | 32 | AY.43 | 0.000142 |
S | 80 | D80A | gAt | gCt | 31 | 31 | B.1.1 | 0.000562 |
S | 80 | D80A | gAt | gCt | 30 | 30 | B.1.1.306 | 0.013152 |
S | 80 | D80A | gAt | gCt | 26 | 26 | B.1.351.1 | 1 |
S | 80 | D80A | gAt | gCt | 24 | 24 | B.1.554 | 0.105727 |
S | 80 | D80A | gAt | gCt | 19 | 19 | AY.61 | 0.001991 |
S | 80 | D80A | gAt | gCt | 16 | 16 | B.1.636 | 0.107383 |
S | 80 | D80A | gAt | gCt | 12 | 12 | AY.44 | 0.000073 |
S | 80 | D80A | gAt | gCt | 12 | 12 | B.1.1.432 | 0.01519 |
S | 80 | D80A | gAt | gCt | 11 | 11 | B.1.177.73 | 0.006229 |
S | 80 | D80A | gAt | gCt | 10 | 10 | AY.59 | 0.005297 |
S | 80 | D80A | gAt | gCt | 10 | 10 | B.1.1.189 | 0.015129 |
S | 80 | D80A | gAt | gCt | 10 | 10 | B.1.1.7 | 0.000009 |
S | 80 | D80A | gAt | gCt | 9 | 9 | AY.19 | 0.010262 |
S | 80 | D80A | gAt | gCt | 9 | 9 | AY.38 | 0.004493 |
S | 80 | D80A | gAt | gCt | 9 | 9 | B.1.1.507 | 0.078261 |
S | 80 | D80A | gAt | gCt | 8 | 8 | AY.75.1 | 0.001442 |
S | 80 | D80A | gAt | gCt | 7 | 7 | AY.26 | 0.000198 |
S | 80 | D80A | gAt | gCt | 7 | 7 | AY.39 | 0.000173 |
S | 80 | D80A | gAt | gCt | 7 | 7 | AY.4 | 0.000011 |
S | 80 | D80A | gAt | gCt | 7 | 7 | AY.71 | 0.003325 |
S | 80 | D80A | gAt | gCt | 7 | 7 | AY.86 | 0.005809 |
S | 80 | D80A | gAt | gCt | 6 | 6 | AY.42 | 0.000241 |
S | 80 | D80A | gAt | gCt | 6 | 6 | AY.56 | 0.009631 |
S | 80 | D80A | gAt | gCt | 6 | 6 | AY.9.2 | 0.00022 |
S | 80 | D80A | gAt | gCt | 6 | 6 | B.1.595 | 0.001566 |
S | 80 | D80A | gAt | gCt | 6 | 6 | B.1.609 | 0.002876 |
S | 80 | D80A | gAt | gCt | 5 | 5 | AY.103 | 0.000031 |
S | 80 | D80A | gAt | gCt | 5 | 5 | AY.36 | 0.000741 |
S | 80 | D80A | gAt | gCt | 5 | 5 | AY.46 | 0.00052 |
S | 80 | D80A | gAt | gCt | 5 | 5 | P.5 | 0.068493 |
S | 80 | D80A | gAt | gCt | 4 | 4 | A | 0.001548 |
S | 80 | D80A | gAt | gCt | 4 | 4 | AY.1 | 0.001583 |
S | 80 | D80A | gAt | gCt | 4 | 4 | AY.23 | 0.000279 |
S | 80 | D80A | gAt | gCt | 4 | 4 | AY.65 | 0.002132 |
S | 80 | D80A | gAt | gCt | 4 | 4 | AY.66 | 0.004278 |
S | 80 | D80A | gAt | gCt | 3 | 4 | AY.91 | 0.002191 |
S | 80 | D80A | gAt | gCt | 4 | 4 | AY.96 | 0.008299 |
S | 80 | D80A | gAt | gCt | 4 | 4 | B.1.1.375 | 0.047619 |
S | 80 | D80A | gAt | gCt | 4 | 4 | B.1.1.409 | 0.011331 |
S | 80 | D80A | gAt | gCt | 4 | 4 | B.1.367 | 0.00317 |
S | 80 | D80A | gAt | gCt | 4 | 4 | B.1.429 | 0.000094 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.116 | 0.00086 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.120.2 | 0.003856 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.14 | 0.000264 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.3 | 0.00003 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.32 | 0.001597 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.40 | 0.002893 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.5 | 0.000062 |
S | 80 | D80A | gAt | gCt | 3 | 3 | AY.75 | 0.000168 |
S | 80 | D80A | gAt | gCt | 3 | 3 | B.1.1.389 | 0.018182 |
S | 80 | D80A | gAt | gCt | 3 | 3 | B.1.1.53 | 0.041096 |
S | 80 | D80A | gAt | gCt | 3 | 3 | B.1.160 | 0.000094 |
S | 80 | D80A | gAt | gCt | 3 | 3 | B.1.177.86 | 0.00055 |
S | 80 | D80A | gAt | gCt | 3 | 3 | P.1 | 0.000047 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.102 | 0.000053 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.117 | 0.000169 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.120 | 0.000074 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.24 | 0.000862 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.29 | 0.000032 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.33 | 0.000134 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.52 | 0.001629 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.53 | 0.000575 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.68 | 0.000547 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.70 | 0.000417 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.92 | 0.000575 |
S | 80 | D80A | gAt | gCt | 2 | 2 | AY.98.1 | 0.000097 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B | 0.000256 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B.1.1.526 | 0.007092 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B.1.177 | 0.000026 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B.1.177.7 | 0.00033 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B.1.214 | 0.007326 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B.1.36 | 0.000292 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B.1.525 | 0.000226 |
S | 80 | D80A | gAt | gCt | 2 | 2 | B.1.617.1 | 0.000258 |
S | 80 | D80A | gAt | gCt | 2 | 2 | R.1 | 0.00018 |
S | 80 | D80A | gAt | gCt | 1 | 1 | A.23.1 | 0.000704 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.10 | 0.00053 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.105 | 0.000643 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.107 | 0.000466 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.115 | 0.005208 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.119 | 0.000035 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.12 | 0.000316 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.121 | 0.000135 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.16.1 | 0.00047 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.22 | 0.002092 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.30 | 0.000396 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.34 | 0.000097 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.47 | 0.000031 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.48 | 0.000465 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.5.3 | 0.000337 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.55 | 0.000917 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.67 | 0.000464 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.7.1 | 0.000113 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.77 | 0.001127 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.79 | 0.001211 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.85 | 0.000427 |
S | 80 | D80A | gAt | gCt | 1 | 1 | AY.94 | 0.000443 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.1 | 0.000327 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.203 | 0.016949 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.220 | 0.001859 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.25 | 0.000569 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.269 | 0.001353 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.372 | 0.000689 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.521 | 0.005348 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.1.523 | 0.001563 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.110.3 | 0.000718 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.139 | 0.000733 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.170 | 0.00431 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.177.42 | 0.000894 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.177.74 | 0.015152 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.240 | 0.000216 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.241 | 0.000812 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.311 | 0.000275 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.399 | 0.001934 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.427 | 0.00005 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.466.2 | 0.000391 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.596 | 0.000087 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.599 | 0.00365 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.600 | 0.005848 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.1.620 | 0.000946 |
S | 80 | D80A | gAt | gCt | 1 | 1 | B.35 | 0.007812 |
S | 80 | D80A | gAt | gCt | 1 | 1 | C.1 | 0.002392 |
S | 80 | D80A | gAt | gCt | 1 | 1 | C.16 | 0.00106 |
S | 80 | D80A | gAt | gCt | 1 | 1 | C.2 | 0.016129 |
S | 80 | D80A | gAt | gCt | 1 | 1 | P.2 | 0.000187 |
S | 80 | D80A | gAt | gCt | 1 | 1 | P.3 | 0.001595 |
CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk
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